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19 protocols using s32354

1

Biotinylation and Immunofluorescence Imaging

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Isolated cardiomyocytes were first exposed to biotin-phenol and H2O2 as described above. After quenching, the cells were fixed for 15 minutes in 4% paraformaldehyde, washed with glycine/PBS (phosphate-buffered saline) twice, treated with PBST (0.1% Triton X-100 (v/v) in PBS) for 5 minutes, and blocked with 3% BSA (w/v) in PBS for 1 hour. Indirect immunofluorescence was performed using dilutions of 1:500 of anti-V5 antibody (Thermofisher, R960-25) and 1:200 of Alexa594-labeled goat-anti-mouse antibody (Thermofisher, A11032, Lot#2069816), and 1:800 of streptavidin-Alexa Fluor 488 conjugate (Thermofisher, S32354, Lot# 1719656). Images were acquired using a confocal microscopy.
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2

Biotinylation and Immunofluorescence Imaging

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Isolated cardiomyocytes were first exposed to biotin-phenol and H2O2 as described above. After quenching, the cells were fixed for 15 minutes in 4% paraformaldehyde, washed with glycine/PBS (phosphate-buffered saline) twice, treated with PBST (0.1% Triton X-100 (v/v) in PBS) for 5 minutes, and blocked with 3% BSA (w/v) in PBS for 1 hour. Indirect immunofluorescence was performed using dilutions of 1:500 of anti-V5 antibody (Thermofisher, R960-25) and 1:200 of Alexa594-labeled goat-anti-mouse antibody (Thermofisher, A11032, Lot#2069816), and 1:800 of streptavidin-Alexa Fluor 488 conjugate (Thermofisher, S32354, Lot# 1719656). Images were acquired using a confocal microscopy.
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3

Immunodetection of B-cell and Plasma-cell Markers

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At day 14, 2D and 3D cultures were fixated in 4% (v/v) buffered formaldehyde (VWR Chemicals) and washed with PBS. Heat-mediated antigen retrieval was performed on all samples, for 15 min at 90°C in 0.5M EDTA buffer pH 8.0 (Invitrogen, ThermoFisher). Cells were permeabilized using 0.2% (v/v) Triton X-100 (Merck Millipore) in PBS for 10 min and washed with PBS. Samples were then blocked with 50 mg/mL BSA in PBS for 1 h at room temperature (RT) and subsequently washed in PBS. Immunodetection was performed by incubation with purified anti-human CD19 antibody (10 μg/mL, SJ25C1, Biolegend) or purified anti-human CD138 antibody (10 μg/mL, MI15, Biolegend) overnight at RT, followed by biotinylated sheep anti-mouse (1:200, RPN1001; GE Healthcare) for 1 h at RT, and Alexa Fluor 488 anti-streptavidin (4 μg/mL, S32354; Thermo Fisher Scientific) for 1 h at RT, all in PBS containing 50 mg/mL BSA and incubated on a plate shaker (150 rpm). All antibodies were centrifuged before use (13,000 rpm for 5 min). Between staining steps, samples were washed in 0.1% Tween 20 (v/v, Merck Millipore) in PBS. Samples were then stained for Phalloidin–Atto 700 (0.4 nmol/mL, 79,286, Sigma Aldrich) and DAPI (100 ng/mL, D9542, Sigma Aldrich), washed in PBS and mounted using Vectashield (Vector Laboratories).
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4

Fluorescence Immunostaining of Tyrosine Hydroxylase

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Immunohistochemistry was performed as described previously (Bateup et al., 2013 (link)). The following antibodies were used: tyrosine hydroxylase (TH, ImmunoStar #22941, RRID:AB_572268), Alexa Fluor 488 goat anti-mouse secondary (Thermo Fisher Scientific #A-11001, RRID:AB_2534069), Alexa Fluor 633 goat anti-mouse secondary (Thermo Fisher Scientific #A-21050, RRID:AB_2535718), streptavidin Alexa Fluor 488 conjugate (Thermo Fisher Scientific #S32354, RRID:AB_2315383), and streptavidin Alexa Fluor 633 conjugate (Thermo Fisher Scientific #S21375, RRID:AB_2313500).
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5

Retrograde Labeling of Zebrafish Spinal Neurons

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Zebrafish were anesthetized in 0.03% tricaine methane sulfonate (MS-222, Sigma-Aldrich, E10521). Retrograde labeling of descending spinal cord neurons located in spinal segments 1–3 was achieved through dye injections with biotinylated dextran (3000 MW; ThermoFisher, D7135) into segment 16 or 17. Animals were kept alive for at least 24 h after injection to allow retrograde transport of the tracer, deeply anesthetized with 0.1% MS-222, and the spinal cords were dissected and fixed in 4% paraformaldehyde (PFA) and 5% saturated picric acid (Sigma-Aldrich, P6744) in phosphate-buffered saline (PBS; 0.01 M, pH = 7.4; Santa Cruz Biotechnology, Inc., CAS30525-89-4) at 4 °C for 4–10 h. The tissue was then washed extensively with PBS and incubated in streptavidin conjugated to Alexa Fluor 488 (dilution 1:500, ThermoFisher, S32354), Alexa Fluor 555 (1:500, ThermoFisher, S32355), or Alexa Fluor 647 (dilution 1:500, ThermoFisher, S32357) overnight at 4 °C. Primary and secondary antibodies were applied as described in the “Immunohistochemistry” section. After thorough buffer rinses, the tissue was mounted on gelatin-coated microscope slides and cover-slipped with an anti-fade fluorescent mounting medium (Vectashield Hard Set, VectorLabs; H-1400).
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6

CST Collateral Staining in Spinal Cord

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To stain hindlimb CST collaterals entering the grey matter at the cervical spinal cord level we cut 50 µm coronal (transverse) sections of the cervical spinal cord (C3–C5) of mice that had a dorsal thoracic hemisection, LPSN labelling and BDA injected in the motor cortex. All sections were first incubated in ABC complex (Vector Laboratories) over night at 4 °C, then washed and incubated with tyramide (Biotin-XX, TSA kit #21, Thermo Fisher Scientific T20931) for 30 min at RT, washed again and incubated with Streptavidin-FITC or -Alexa488 for 2 h at RT (1:500, Thermo Fisher Scientific, SA10002 and S32354). To quantify CST regenerative sprouting at the lesion site, longitudinal consecutive sections from the lesion site were cut (40 µm) and stained as described above.
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7

Immunofluorescence Detection of BioID2 Fusion Proteins

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Cells grown on 1.5 mm glass coverslips were fixed with 3% (w/v) paraformaldehyde/phosphate-buffered saline for 10 min and permeabilized with 0.4% (w/v) Triton X −100/PBS for 15 min. To detect BioID2 fusion proteins, chicken anti-BioID2 (1:5000; BID2-CP-100; BioFront Technologies) was used (18 (link)). The anti-BioID2 antibody was detected using Alexa Fluor 568–conjugated goat anti-chicken (1:1000; A11041; Thermo Fisher Scientific). Alexa Fluor 488–conjugated streptavidin (1:1000; S32354; Thermo Fisher Scientific) was used to detect biotinylated proteins. DNA was detected with Hoechst dye 33342. Coverslips were mounted using 10% (wt/vol) Mowiol 4 to 88 (Polysciences). Epifluorescence images were obtained using a Nikon Eclipse NiE microscope (40 × /0.75 Plan Apo Nikon objective) with a charge-coupled device camera (CoolSnap HQ; Photometrics) linked to a workstation running NIS-Elements software (Nikon). All images were processed in Adobe Photoshop CC 2023 (https://www.techspot.com/downloads/6043-adobe-creative-cloud-photoshop.html) (Adobe) for cropping and brightness/contrast adjustment when applicable.
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8

Immunofluorescence Staining and Microscopy

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Cells grown on glass coverslips were fixed in 3% (wt/vol) paraformaldehyde/phosphate-buffered saline (PBS) for 10 min and permeabilized by 0.4% (wt/vol) Triton X-100/PBS for 15 min. For labeling fusion proteins, chicken anti-BioID2 (1:5000; BID2-CP-100; BioFront Technologies, Tallahassee, FL, USA) or mouse anti-hemagglutinin primary antibody was used (HA; 1:1000; 12CA5; Covance, Princeton, NJ, USA). The primary antibody was detected using Alexa Fluor 568–conjugated goat anti-chicken (1:1000; ab175477, Lot#GR144853-2, Abcam, Cambridge, United Kingdom) or Alexa Fluor 568–conjugated goat anti-mouse (1:1000; A11004; Lot#1698376, Thermo Fisher Scientific). Alexa Fluor 488–conjugated streptavidin (1:1000; S32354; Lot#2201616, Thermo Fisher Scientific) was used to detect biotinylated proteins. DNA was detected with Hoechst dye 33342. Coverslips were mounted using 10% (wt/vol) Mowiol 4-88 (Polysciences, Warrington, PA, USA). Epifluorescence images were captured using a Nikon Eclipse NiE (40 ×/0.75 Plan Apo Nikon objective, Minato City, Tokyo, Japan) microscope.
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9

Immunofluorescent Labeling of Nasal Tissue

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After decapitation, the head was immediately put into 4% paraformaldehyde (Sigma) overnight at 4 °C, and then subject to decalcification in 0.5 M EDTA (pH 8.0, ethylenediaminetetraacetic acid) for two days. The nose was cut into 20 μm coronal sections on a cryostat. After antigen retrieval in 95 °C waterbath for 12 min, nose sections were first blocked for 60 min in TPBS (0.3% Triton X-100 in phosphate buffered saline) with 2% bovine serum albumin and then incubated at 4 °C with the primary antibodies in the same solution for overnight. Immunofluorescence was achieved by reaction with appropriate secondary antibodies at 1:400 for 1 hr. Tissues were washed in TPBS and mounted in Vectashield (Vector Laboratories). Pictures were taken under a Zeiss LSM 510 confocal microscope. The primary antibodies included biotinylated Dolichos Biflorus Agglutinin (DBA, 1:300, B-1035, Vector Laboratories) and rabbit anit-M3-R (1:300, M0194, Sigma-Aldrich), and the secondary antibodies included streptavidin conjugate 488 (S-32354, Invitrogen) and donkey-anti-rabbit-568 (A10042, Invitrogen). DAPI (4′,6-diamidino-2-phenylindole, Dihydrochloride) (D1306, Invitrogen) was used to stain the cell nuclei.
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10

Immunofluorescence Imaging of FLAG-Tagged Proteins

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Flp-In T-REx HEK293 cells stably expressing 3XFLAG or BirA*-FLAG tagged proteins were seeded on poly-L-lysine coated cover slips (product #354085;BD Biosciences) at low density and grown in complete medium for 24 hours. Cells were fixed with 3.7% paraformaldehyde/PBS and permeabilized in 0.3% Triton X-100 in PBS. Mouse anti-FLAG M2 antibody (1:2000; F1804, Sigma-Aldrich), rabbit anti-FLAG antibody (1:1000; F7425, Sigma-Aldrich), mouse anti-centrin (1:1000, 04-1624, EMD Millipore), rabbit anti-pericentrin (1:2000, ab4448, Abcam) and streptavidin Alexa-Fluor 488 (1:2500; S32354; Invitrogen) were used to identify FLAG tagged proteins and biotinylated proteins, respectively. Proteins were visualized with goat anti-mouse or anti-rabbit coupled to Alexa-Fluor 488 or 555 antibodies (1:1,000; A11001, A11008, A21422, A21428; Invitrogen). DNA was detected with DAPI staining. Immunofluorescence was observed by confocal microscopy on a Nikon Eclipse C1si instrument.
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